Purpose Prisons in the sub-Saharan African region face unprecedented challenges during the COVID-19 pandemic. In Malawi, the first prison system case of COVID-19 was notified in July 2020. While prison settings were included in the second domestic COVID-19 response plan within the Law Enforcement cluster (National COVID-19 preparedness and response plan, July–December 2020), they were initially not included in the K157bn (US$210m) COVID-19 fund. The purpose of the study was to assess prison preparedness, prevention and control of COVID-19 in Malawi.. Design/methodology/approach A multi-method situation assessment of the COVID-19 response and human rights assurance of prisoners and staff was conducted in a large prison complex in Malawi. Qualitative research underpinned by the Empirical Phenomenological Psychological (EPP) framework consisted of interviews with key informants such as prison health personnel, senior prison staff, penal and judicial policymakers, government and civil society organisations (n = 14) and focus group discussions with consenting male (n = 48) and female prisoners (n = 48) and prison wardens (n = 24). Prison site visits were supported by detailed observations based on the World Health Organisation Checklist for COVID-19 in prisons (n = 9). Data were collected and analysed thematically using the EPP stepwise approach and triangulated based on Bronfenbrenner’s model conceptualising COVID-19 as a multi-level event disrupting the prison eco-system. Findings The results are presented as MICRO-MESO level individual and community experiences of incarceration during COVID-19 spanning several themes: awareness raising and knowledge of COVID-19 in prisons; prison congestion and the impossibility of social distancing; lack of adequate ventilation, hygiene and sanitation and provisions and correct use of personal protective equipment; MESO-MACRO level interplay between the prison community of prisoners and staff and judicial policy impacts; medical system COVID-19 response, infrastructure and access to health care; COVID-19 detection and quarantine measures and prisoner access to the outside world. Originality/value This unique situation assessment of the Malawian prison system response to mitigate COVID-19 illustrates the dynamics at the micro-level whereby prisoners rely on the state and have restricted agency in protecting themselves from disease. This is due to severe structural inadequacies based on low resource allocation to prisons leading to a compromised ability to prevent and treat disease; an infirm and congested infrastructure and bottlenecks in the judicial system fuelling a continued influx of remand detainees leading to high overcapacity. Multi-pronged interventions involving key stakeholders, with prison management and line Ministry as coordinators are warranted to optimise COVID-19 interventions and future disease outbreaks in the Malawian prison system.

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